def run_roa(name, **kwargs):
# Get list of omega values -> Make sure we only have one wavelength
# Catch this now before any real work gets done
omega = psi4.get_option('CCRESPONSE','OMEGA')
if len(omega) > 2:
raise Exception('ROA scattering can only be performed for one wavelength.')
else:
pass
psi4.print_out('Running ROA computation. Subdirectories for each '
'required displaced geometry have been created.\n\n')
### Initialize database
db = shelve.open('database',writeback=True)
if 'inputs_generated' not in db:
initialize_database(db)
### Generate input files
if not db['inputs_generated']:
generate_inputs(name, db)
db['inputs_generated'] = True
### If 'serial' calculation, proceed with subdir execution
### Check job status
if db['inputs_generated'] and not db['jobs_complete']:
print('Checking status')
roa_stat(db)
for job,status in db['job_status'].items():
print("{} --> {}".format(job,status))
### Compute ROA Scattering
if db['jobs_complete']:
# SAVE this for when multiple wavelengths works
# # Get list of omega values
# omega = psi4.get_option('CCRESPONSE','OMEGA')
# if len(omega) > 1:
# units = copy.copy(omega[-1])
# omega.pop()
# else:
# units = 'atomic'
# wavelength = copy.copy(omega[0])
# # Set up units for scatter.cc
# if units == 'NM':
# wavelength = (psi_c * psi_h * 1*(10**-9))/(wavelength * psi_hartree2J)
# if units == 'HZ':
# wavelength = wavelength * psi_h / psi_hartree2J
# if units == 'EV':
# wavelength = wavelength / psi_hartree2ev
# if units == 'atomic':
# pass
# Initialize tensor lists
dip_polar_list = []
opt_rot_list = []
dip_quad_polar_list = []
gauge_list = []
make_gauge_list(gauge_list)
# Gather data
synthesize_dipole_polar(db,dip_polar_list)
synthesize_opt_rot(db,opt_rot_list)
synthesize_dip_quad_polar(db,dip_quad_polar_list)
# Compute Scattering
# Run new function (src/bin/ccresponse/scatter.cc)
psi4.print_out('Running scatter function')
step = psi4.get_local_option('FINDIF','DISP_SIZE')
for gauge in opt_rot_list:
g_idx = opt_rot_list.index(gauge)
# print('\n\n----------------------------------------------------------------------')
# print('\t%%%%%%%%%% {} %%%%%%%%%%'.format(gauge_list[g_idx]))
# print('----------------------------------------------------------------------\n\n')
psi4.print_out('\n\n----------------------------------------------------------------------\n')
psi4.print_out('\t%%%%%%%%%% {} %%%%%%%%%%\n'.format(gauge_list[g_idx]))
psi4.print_out('----------------------------------------------------------------------\n\n')
print('roa.py:85 I am not being passed a molecule, grabbing from global :(')
psi4.scatter(psi4.get_active_molecule(), step, dip_polar_list, gauge, dip_quad_polar_list)
db.close()
def run_roa(name, **kwargs):
"""
Main driver for managing Raman Optical activity computations with
CC response theory.
Uses distributed finite differences approach -->
1. Sets up a database to keep track of running/finished/waiting
computations.
2. Generates separate input files for displaced geometries.
3. When all displacements are run, collects the necessary information
from each displaced computation, and computes final result.
"""
# Get list of omega values -> Make sure we only have one wavelength
# Catch this now before any real work gets done
omega = psi4.get_option('CCRESPONSE', 'OMEGA')
if len(omega) > 2:
raise Exception(
'ROA scattering can only be performed for one wavelength.')
else:
pass
psi4.print_out('Running ROA computation. Subdirectories for each '
'required displaced geometry have been created.\n\n')
dbno = 0
# Initialize database
db = shelve.open('database', writeback=True)
# Check if final result is in here
# ->if we have already computed roa, back up the dict
# ->copy it setting this flag to false and continue
if ('roa_computed' in db) and (db['roa_computed']):
db2 = shelve.open('.database.bak{}'.format(dbno), writeback=True)
dbno += 1
for key, value in db.iteritems():
db2[key] = value
db2.close()
db['roa_computed'] = False
else:
db['roa_computed'] = False
if 'inputs_generated' not in db:
findif_response_utils.initialize_database(db, name, "roa",
["roa_tensor"])
# Generate input files
if not db['inputs_generated']:
findif_response_utils.generate_inputs(db, name)
# handled by helper db['inputs_generated'] = True
# Check job status
if db['inputs_generated'] and not db['jobs_complete']:
print('Checking status')
findif_response_utils.stat(db)
for job, status in db['job_status'].items():
print("{} --> {}".format(job, status))
# Compute ROA Scattering
if db['jobs_complete']:
mygauge = psi4.get_option('CCRESPONSE', 'GAUGE')
consider_gauge = {
'LENGTH': ['Length Gauge'],
'VELOCITY': ['Modified Velocity Gauge'],
'BOTH': ['Length Gauge', 'Modified Velocity Gauge']
}
gauge_list = ["{} Results".format(x) for x in consider_gauge[mygauge]]
# Gather data
dip_polar_list = findif_response_utils.collect_displaced_matrix_data(
db, 'Dipole Polarizability', 3)
opt_rot_list = [
x for x in (findif_response_utils.collect_displaced_matrix_data(
db, "Optical Rotation Tensor ({})".format(gauge), 3)
for gauge in consider_gauge[mygauge])
]
dip_quad_polar_list = findif_response_utils.collect_displaced_matrix_data(
db, "Electric-Dipole/Quadrupole Polarizability", 9)
# Compute Scattering
# Run new function (src/bin/ccresponse/scatter.cc)
psi4.print_out('Running scatter function')
step = psi4.get_local_option('FINDIF', 'DISP_SIZE')
for g_idx, gauge in enumerate(opt_rot_list):
print(
'\n\n----------------------------------------------------------------------'
)
print('\t%%%%%%%%%% {} %%%%%%%%%%'.format(gauge_list[g_idx]))
print(
'----------------------------------------------------------------------\n\n'
)
psi4.print_out(
'\n\n----------------------------------------------------------------------\n'
)
psi4.print_out('\t%%%%%%%%%% {} %%%%%%%%%%\n'.format(
gauge_list[g_idx]))
psi4.print_out(
'----------------------------------------------------------------------\n\n'
)
print(
'roa.py:85 I am not being passed a molecule, grabbing from global :('
)
psi4.scatter(psi4.get_active_molecule(), step, dip_polar_list,
gauge, dip_quad_polar_list)
db['roa_computed'] = True
db.close()
def run_roa(name, **kwargs):
# Get list of omega values -> Make sure we only have one wavelength
# Catch this now before any real work gets done
omega = psi4.get_option('CCRESPONSE', 'OMEGA')
if len(omega) > 2:
raise Exception(
'ROA scattering can only be performed for one wavelength.')
else:
pass
psi4.print_out('Running ROA computation. Subdirectories for each '
'required displaced geometry have been created.\n\n')
### Initialize database
db = shelve.open('database', writeback=True)
if 'inputs_generated' not in db:
initialize_database(db)
### Generate input files
if not db['inputs_generated']:
generate_inputs(name, db)
db['inputs_generated'] = True
### If 'serial' calculation, proceed with subdir execution
### Check job status
if db['inputs_generated'] and not db['jobs_complete']:
print('Checking status')
roa_stat(db)
for job, status in db['job_status'].items():
print("{} --> {}".format(job, status))
### Compute ROA Scattering
if db['jobs_complete']:
# SAVE this for when multiple wavelengths works
# # Get list of omega values
# omega = psi4.get_option('CCRESPONSE','OMEGA')
# if len(omega) > 1:
# units = copy.copy(omega[-1])
# omega.pop()
# else:
# units = 'atomic'
# wavelength = copy.copy(omega[0])
# # Set up units for scatter.cc
# if units == 'NM':
# wavelength = (psi_c * psi_h * 1*(10**-9))/(wavelength * psi_hartree2J)
# if units == 'HZ':
# wavelength = wavelength * psi_h / psi_hartree2J
# if units == 'EV':
# wavelength = wavelength / psi_hartree2ev
# if units == 'atomic':
# pass
# Initialize tensor lists
dip_polar_list = []
opt_rot_list = []
dip_quad_polar_list = []
gauge_list = []
make_gauge_list(gauge_list)
# Gather data
synthesize_dipole_polar(db, dip_polar_list)
synthesize_opt_rot(db, opt_rot_list)
synthesize_dip_quad_polar(db, dip_quad_polar_list)
# Compute Scattering
# Run new function (src/bin/ccresponse/scatter.cc)
psi4.print_out('Running scatter function')
step = psi4.get_local_option('FINDIF', 'DISP_SIZE')
for gauge in opt_rot_list:
g_idx = opt_rot_list.index(gauge)
# print('\n\n----------------------------------------------------------------------')
# print('\t%%%%%%%%%% {} %%%%%%%%%%'.format(gauge_list[g_idx]))
# print('----------------------------------------------------------------------\n\n')
psi4.print_out(
'\n\n----------------------------------------------------------------------\n'
)
psi4.print_out('\t%%%%%%%%%% {} %%%%%%%%%%\n'.format(
gauge_list[g_idx]))
psi4.print_out(
'----------------------------------------------------------------------\n\n'
)
psi4.scatter(step, dip_polar_list, gauge, dip_quad_polar_list)
db.close()
def run_roa(name, **kwargs):
"""
Main driver for managing Raman Optical activity computations with
CC response theory.
Uses distributed finite differences approach -->
1. Sets up a database to keep track of running/finished/waiting
computations.
2. Generates separate input files for displaced geometries.
3. When all displacements are run, collects the necessary information
from each displaced computation, and computes final result.
"""
# Get list of omega values -> Make sure we only have one wavelength
# Catch this now before any real work gets done
omega = psi4.get_option('CCRESPONSE', 'OMEGA')
if len(omega) > 2:
raise Exception('ROA scattering can only be performed for one wavelength.')
else:
pass
psi4.print_out(
'Running ROA computation. Subdirectories for each '
'required displaced geometry have been created.\n\n')
dbno = 0
# Initialize database
db = shelve.open('database', writeback=True)
# Check if final result is in here
# ->if we have already computed roa, back up the dict
# ->copy it setting this flag to false and continue
if ('roa_computed' in db) and ( db['roa_computed'] ):
db2 = shelve.open('.database.bak{}'.format(dbno), writeback=True)
dbno += 1
for key,value in db.iteritems():
db2[key]=value
db2.close()
db['roa_computed'] = False
else:
db['roa_computed'] = False
if 'inputs_generated' not in db:
findif_response_utils.initialize_database(db,name,"roa", ["roa_tensor"])
# Generate input files
if not db['inputs_generated']:
findif_response_utils.generate_inputs(db,name)
# handled by helper db['inputs_generated'] = True
# Check job status
if db['inputs_generated'] and not db['jobs_complete']:
print('Checking status')
findif_response_utils.stat(db)
for job, status in db['job_status'].items():
print("{} --> {}".format(job, status))
# Compute ROA Scattering
if db['jobs_complete']:
mygauge = psi4.get_option('CCRESPONSE', 'GAUGE')
consider_gauge = {
'LENGTH': ['Length Gauge'],
'VELOCITY': ['Modified Velocity Gauge'],
'BOTH': ['Length Gauge', 'Modified Velocity Gauge']
}
gauge_list = ["{} Results".format(x) for x in consider_gauge[mygauge]]
# Gather data
dip_polar_list = findif_response_utils.collect_displaced_matrix_data(
db, 'Dipole Polarizability', 3)
opt_rot_list = [
x for x in (
findif_response_utils.collect_displaced_matrix_data(
db,
"Optical Rotation Tensor ({})".format(gauge),
3
)
for gauge in consider_gauge[mygauge]
)
]
dip_quad_polar_list = findif_response_utils.collect_displaced_matrix_data(
db, "Electric-Dipole/Quadrupole Polarizability", 9)
# Compute Scattering
# Run new function (src/bin/ccresponse/scatter.cc)
psi4.print_out('Running scatter function')
step = psi4.get_local_option('FINDIF', 'DISP_SIZE')
for g_idx, gauge in enumerate(opt_rot_list):
print('\n\n----------------------------------------------------------------------')
print('\t%%%%%%%%%% {} %%%%%%%%%%'.format(gauge_list[g_idx]))
print('----------------------------------------------------------------------\n\n')
psi4.print_out('\n\n----------------------------------------------------------------------\n')
psi4.print_out('\t%%%%%%%%%% {} %%%%%%%%%%\n'.format(gauge_list[g_idx]))
psi4.print_out('----------------------------------------------------------------------\n\n')
print('roa.py:85 I am not being passed a molecule, grabbing from global :(')
psi4.scatter(psi4.get_active_molecule(), step, dip_polar_list, gauge, dip_quad_polar_list)
db['roa_computed'] = True
db.close()